Read the Docs build information Build id: 127240 Project: cyverse-cybercarpentry-container-workshop-2018 Version: latest Commit: 538df9c891492eba62ba481157564f1f37412ae3 Date: 2018-07-18T04:42:03.642727Z State: finished Success: True [rtd-command-info] start-time: 2018-07-18T09:42:20.220076Z, end-time: 2018-07-18T09:42:20.229450Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/CyVerse-learning-materials/cybercarpentry_container_workshop_2018.git [rtd-command-info] start-time: 2018-07-18T09:42:20.292477Z, end-time: 2018-07-18T09:42:20.524956Z, duration: 0, exit-code: 0 git fetch --tags --prune [rtd-command-info] start-time: 2018-07-18T09:42:20.592899Z, end-time: 2018-07-18T09:42:20.660486Z, duration: 0, exit-code: 0 git checkout --force origin/master HEAD is now at 538df9c... Add files [rtd-command-info] start-time: 2018-07-18T09:42:20.714871Z, end-time: 2018-07-18T09:42:20.738041Z, duration: 0, exit-code: 0 git clean -d -f -f Removing _build/doctrees-epub/ Removing _build/doctrees-json/ Removing _build/doctrees-readthedocs/ Removing _build/doctrees-readthedocssinglehtmllocalmedia/ Removing _build/doctrees/images/ Removing _build/epub/ Removing _build/html/_static/fonts/Lato/ Removing _build/html/_static/fonts/RobotoSlab/ Removing _build/html/_static/readthedocs-data.js Removing _build/json/ Removing _build/latex/ Removing _build/localmedia/ Removing misc/__init__.pyc Removing misc/cyverse_sphinx_conf.pyc [rtd-command-info] start-time: 2018-07-18T09:42:20.840491Z, end-time: 2018-07-18T09:42:20.846531Z, duration: 0, exit-code: 0 git branch -r origin/HEAD -> origin/master origin/master [rtd-command-info] start-time: 2018-07-18T09:42:21.423783Z, end-time: 2018-07-18T09:42:23.023244Z, duration: 1, exit-code: 0 python2.7 -mvirtualenv --no-site-packages --no-download New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/bin/python2.7 Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/bin/python2.7) Installing setuptools, pip, wheel...done. [rtd-command-info] start-time: 2018-07-18T09:42:23.096801Z, end-time: 2018-07-18T09:42:25.081540Z, duration: 1, exit-code: 0 python pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/.cache/pip Pygments==2.2.0 setuptools<40 docutils==0.13.1 mock==1.0.1 pillow==2.6.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.4.0 sphinx<1.8 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<0.6 Requirement already up-to-date: Pygments==2.2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: setuptools<40 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: docutils==0.13.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: mock==1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: pillow==2.6.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: commonmark==0.5.4 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: recommonmark==0.4.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: sphinx<1.8 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: sphinx-rtd-theme<0.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: readthedocs-sphinx-ext<0.6 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages Requirement already up-to-date: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Requirement already up-to-date: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Requirement already up-to-date: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Requirement already up-to-date: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Requirement already up-to-date: typing; python_version < "3.5" in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Requirement already up-to-date: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Requirement already up-to-date: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Requirement already up-to-date: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Requirement already up-to-date: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx<1.8) Requirement already up-to-date: idna<2.8,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8) Requirement already up-to-date: urllib3<1.24,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8) Requirement already up-to-date: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8) Requirement already up-to-date: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8) Requirement already up-to-date: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from packaging->sphinx<1.8) Requirement already up-to-date: pytz>=0a in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from babel!=2.0,>=1.3->sphinx<1.8) Requirement already up-to-date: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from Jinja2>=2.3->sphinx<1.8) You are using pip version 9.0.1, however version 10.0.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. [rtd-command-info] start-time: 2018-07-18T09:42:25.141193Z, end-time: 2018-07-18T09:42:25.700874Z, duration: 0, exit-code: 0 python pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/.cache/pip -r/home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/requirements.txt Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from -r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: recommonmark in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from -r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/requirements.txt (line 2)) Requirement already satisfied: sphinxcontrib-images in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from -r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/requirements.txt (line 3)) Requirement already satisfied: sphinx_bootstrap_theme in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from -r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/requirements.txt (line 4)) Requirement already satisfied: guzzle_sphinx_theme==0.7.11 in 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satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: typing; python_version < "3.5" in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: commonmark<=0.5.4 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from recommonmark->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/requirements.txt (line 2)) Requirement already satisfied: idna<2.8,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: urllib3<1.24,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r 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/home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from packaging->sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: pytz>=0a in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from babel!=2.0,>=1.3->sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/requirements.txt (line 1)) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/envs/latest/lib/python2.7/site-packages (from Jinja2>=2.3->sphinx->-r /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/requirements.txt (line 1)) You are using pip version 9.0.1, however version 10.0.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. [rtd-command-info] start-time: 2018-07-18T09:42:26.188909Z, end-time: 2018-07-18T09:42:26.254138Z, duration: 0, exit-code: 0 cat conf.py #!/usr/bin/env python3 # -*- coding: utf-8 -*- # # General information about the project. import sys import os sys.path.insert(0, os.path.dirname(__file__)) from misc.cyverse_sphinx_conf import * # noqa project = 'Cybercarpentry_workshop_2018' copyright = '2018, CyVerse' author = 'CyVerse' version = '0.1.0' release = '0.1.0' epub_title = project epub_author = author epub_publisher = author epub_copyright = copyright ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix else: SUFFIX = source_suffix[0] else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') html_static_path.append('/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = False if 'html_theme' in globals(): if html_theme in ['default']: # Allow people to bail with a hack of having an html_style if not 'html_style' in globals(): import sphinx_rtd_theme html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(sphinx_rtd_theme.get_html_theme_path()) else: html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] using_rtd_theme = True else: import sphinx_rtd_theme html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(sphinx_rtd_theme.get_html_theme_path()) else: html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] using_rtd_theme = True if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' if 'http' not in settings.MEDIA_URL: websupport2_static_url = 'https://media.readthedocs.com/' else: websupport2_static_url = 'https://media.readthedocs.com/media//static' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("pdf", "//readthedocs.com/projects/cyverse-cybercarpentry-container-workshop-2018/downloads/pdf/latest/"), ("htmlzip", "//readthedocs.com/projects/cyverse-cybercarpentry-container-workshop-2018/downloads/htmlzip/latest/"), ("epub", "//readthedocs.com/projects/cyverse-cybercarpentry-container-workshop-2018/downloads/epub/latest/"), ], 'subprojects': [ ], 'slug': 'cyverse-cybercarpentry-container-workshop-2018', 'name': u'cybercarpentry_container_workshop_2018', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://cyverse-cybercarpentry-container-workshop-2018.readthedocs-hosted.com/en/latest/', 'analytics_code': '', 'single_version': False, 'conf_py_path': '/./', 'api_host': 'https://readthedocs.com', 'github_user': 'CyVerse-learning-materials', 'github_repo': 'cybercarpentry_container_workshop_2018', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '538df9c8', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Build the json artifacts with the html build step rtd_generate_json_artifacts = False [rtd-command-info] start-time: 2018-07-18T09:42:26.318344Z, end-time: 2018-07-18T09:42:28.426915Z, duration: 2, exit-code: 0 python sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.7.6 loading translations [en]... done making output directory... loading pickled environment... not yet created building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 14 source files that are out of date updating environment: 14 added, 0 changed, 0 removed reading sources... [ 7%] atmosphere/boot reading sources... [ 14%] docker/dockeradvanced reading sources... [ 21%] docker/dockerdemos reading sources... [ 28%] docker/dockerintro reading sources... [ 35%] getting_started/about_cyverse reading sources... [ 42%] getting_started/agenda reading sources... [ 50%] getting_started/installation reading sources... [ 57%] getting_started/main reading sources... [ 64%] index reading sources... [ 71%] singularity/singularityadvanced reading sources... [ 78%] singularity/singularityintro reading sources... [ 85%] useful_resources/usefulresources_docker reading sources... [ 92%] useful_resources/usefulresources_other reading sources... [100%] useful_resources/usefulresources_singularity /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/docker/dockerdemos.rst:9: WARNING: Title underline too short. 1. Play-with-docker (PWD) ======================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/docker/dockerintro.rst:2: WARNING: Duplicate explicit target name: "dockerfile". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/docker/dockerintro.rst:351: WARNING: Title level inconsistent: 5.1 Public repositories ~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/docker/dockerintro.rst:2: WARNING: Duplicate explicit target name: "docker hub". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/singularity/singularityadvanced.rst:23: WARNING: Content block expected for the "Note" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/singularity/singularityadvanced.rst:42: WARNING: Content block expected for the "Note" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/singularity/singularityintro.rst:492: WARNING: Title underline too short. 4.1: Docker2Singularity & Singularity2Docker ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity-hub". looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... 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Highlighting skipped. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/singularity/singularityintro.rst:110: WARNING: Could not lex literal_block as "bash". Highlighting skipped. generating indices... genindex writing additional pages... search copying images... [ 2%] docker/../img/auto_build-1.png copying images... [ 5%] docker/../img/bind_mount.png copying images... [ 8%] atmosphere/../img/atmo-1.png copying images... [ 10%] docker/../img/dc-1.png copying images... [ 13%] docker/../img/r_kernel.png copying images... [ 16%] docker/../img/docker.jpg copying images... [ 18%] docker/../img/rstudio_login.png copying images... [ 21%] docker/../img/auto-6.png copying images... [ 24%] atmosphere/../img/atmo_cp.png copying images... [ 27%] docker/../img/auto-2.png copying images... [ 29%] docker/../img/rstudio-2.png copying images... [ 32%] docker/../img/jn_login2.png copying images... 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[rtd-command-info] start-time: 2018-07-18T09:42:28.531285Z, end-time: 2018-07-18T09:42:30.312923Z, duration: 1, exit-code: 0 python sphinx-build -T -b json -d _build/doctrees-json -D language=en . _build/json Running Sphinx v1.7.6 loading translations [en]... done making output directory... loading pickled environment... not yet created building [mo]: targets for 0 po files that are out of date building [json]: targets for 14 source files that are out of date updating environment: 14 added, 0 changed, 0 removed reading sources... [ 7%] atmosphere/boot reading sources... [ 14%] docker/dockeradvanced reading sources... [ 21%] docker/dockerdemos reading sources... [ 28%] docker/dockerintro reading sources... [ 35%] getting_started/about_cyverse reading sources... [ 42%] getting_started/agenda reading sources... [ 50%] getting_started/installation reading sources... [ 57%] getting_started/main reading sources... [ 64%] index reading sources... 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Play-with-docker (PWD) ======================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/docker/dockerintro.rst:2: WARNING: Duplicate explicit target name: "dockerfile". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/docker/dockerintro.rst:351: WARNING: Title level inconsistent: 5.1 Public repositories ~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/docker/dockerintro.rst:2: WARNING: Duplicate explicit target name: "docker hub". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/singularity/singularityadvanced.rst:23: WARNING: Content block expected for the "Note" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/singularity/singularityadvanced.rst:42: WARNING: Content block expected for the "Note" directive; none found. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/singularity/singularityintro.rst:492: WARNING: Title underline too short. 4.1: Docker2Singularity & Singularity2Docker ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity-hub". looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... 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Highlighting skipped. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/singularity/singularityintro.rst:110: WARNING: Could not lex literal_block as "bash". Highlighting skipped. generating indices... genindex writing additional pages... search copying images... [ 2%] docker/../img/auto_build-1.png copying images... [ 5%] docker/../img/bind_mount.png copying images... [ 8%] atmosphere/../img/atmo-1.png copying images... [ 10%] docker/../img/dc-1.png copying images... [ 13%] docker/../img/r_kernel.png copying images... [ 16%] docker/../img/docker.jpg copying images... [ 18%] docker/../img/rstudio_login.png copying images... [ 21%] docker/../img/auto-6.png copying images... [ 24%] atmosphere/../img/atmo_cp.png copying images... [ 27%] docker/../img/auto-2.png copying images... [ 29%] docker/../img/rstudio-2.png copying images... [ 32%] docker/../img/jn_login2.png copying images... 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[rtd-command-info] start-time: 2018-07-18T09:42:30.418123Z, end-time: 2018-07-18T09:42:32.221276Z, duration: 1, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.7.6 loading translations [en]... done making output directory... loading pickled environment... not yet created building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 14 added, 0 changed, 0 removed reading sources... [ 7%] atmosphere/boot reading sources... [ 14%] docker/dockeradvanced reading sources... [ 21%] docker/dockerdemos reading sources... [ 28%] docker/dockerintro reading sources... [ 35%] getting_started/about_cyverse reading sources... [ 42%] getting_started/agenda reading sources... [ 50%] getting_started/installation reading sources... [ 57%] getting_started/main reading sources... 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[rtd-command-info] start-time: 2018-07-18T09:42:32.345348Z, end-time: 2018-07-18T09:42:34.155241Z, duration: 1, exit-code: 0 python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v1.7.6 loading translations [en]... done making output directory... loading pickled environment... failed: unsupported pickle protocol: 4 building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 14 added, 0 changed, 0 removed reading sources... [ 7%] atmosphere/boot reading sources... [ 14%] docker/dockeradvanced reading sources... [ 21%] docker/dockerdemos reading sources... [ 28%] docker/dockerintro reading sources... [ 35%] getting_started/about_cyverse reading sources... [ 42%] getting_started/agenda reading sources... [ 50%] getting_started/installation reading sources... [ 57%] getting_started/main reading sources... [ 64%] index reading sources... [ 71%] singularity/singularityadvanced reading sources... 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[rtd-command-info] start-time: 2018-07-18T09:42:34.216205Z, end-time: 2018-07-18T09:42:41.222660Z, duration: 7, exit-code: 0 pdflatex -interaction=nonstopmode /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/_build/latex/CyVerseDocumentation.tex This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (/home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-contai ner-workshop-2018/checkouts/latest/_build/latex/CyVerseDocumentation.tex LaTeX2e <2016/02/01> Babel <3.9q> and hyphenation patterns for 81 language(s) loaded. 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Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 2687. [77] [78] Chapter 12. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 2730. [79] [80] Chapter 13. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 2750. No file CyVerseDocumentation.ind. [81] (./CyVerseDocumentation.aux) Package rerunfilecheck Warning: File `CyVerseDocumentation.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on CyVerseDocumentation.pdf (85 pages, 3607514 bytes). Transcript written on CyVerseDocumentation.log. [rtd-command-info] start-time: 2018-07-18T09:42:41.280897Z, end-time: 2018-07-18T09:42:41.415153Z, duration: 0, exit-code: 0 makeindex -s python.ist CyVerseDocumentation.idx This is makeindex, version 2.15 [TeX Live 2015] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file CyVerseDocumentation.idx...done (0 entries accepted, 0 rejected). Nothing written in CyVerseDocumentation.ind. Transcript written in CyVerseDocumentation.ilg. [rtd-command-info] start-time: 2018-07-18T09:42:41.476992Z, end-time: 2018-07-18T09:42:48.496602Z, duration: 7, exit-code: 0 pdflatex -interaction=nonstopmode /home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-container-workshop-2018/checkouts/latest/_build/latex/CyVerseDocumentation.tex This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (/home/docs/checkouts/readthedocs.org/user_builds/cyverse-cybercarpentry-contai ner-workshop-2018/checkouts/latest/_build/latex/CyVerseDocumentation.tex LaTeX2e <2016/02/01> Babel <3.9q> and hyphenation patterns for 81 language(s) loaded. 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(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) Writing index file CyVerseDocumentation.idx (./CyVerseDocumentation.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./CyVerseDocumentation.out) (./CyVerseDocumentation.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (./CyVerseDocumentation.toc) [1] [2] [1 <./cyverse_rgb.png>] [2] Chapter 1. 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Underfull \hbox (badness 10000) in paragraph at lines 271--272 []|\T1/ptm/m/n/10 Introduction to Docker Underfull \hbox (badness 10000) in paragraph at lines 295--296 []|\T1/ptm/m/n/10 General overview of Underfull \hbox (badness 10000) in paragraph at lines 295--296 \T1/ptm/m/n/10 Sin-gu-lar-ity (Up-en-dra Underfull \hbox (badness 10000) in paragraph at lines 2--299 [][][]\T1/ptm/m/n/10 Singularity [7] [8] Chapter 4. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 311. [9] [10] Chapter 5. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 345. 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[35 <./jn_login3.5.png> <./r_kernel.png>] Overfull \hbox (94.8493pt too wide) in paragraph at lines 1270--1271 [] Overfull \hbox (94.82553pt too wide) in paragraph at lines 1284--1285 [] [36 <./rstudio_ss.png>] Overfull \hbox (94.82121pt too wide) in paragraph at lines 1288--1289 [] Overfull \hbox (94.8618pt too wide) in paragraph at lines 1292--1293 [] [37 <./rstudio_login2.png> <./rstudio_login.png>] Overfull \hbox (94.8701pt too wide) in paragraph at lines 1294--1295 [] [38 <./rstudio-2.png> <./rstudio-3.png>] Chapter 7. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 1297. Overfull \hbox (94.82858pt too wide) in paragraph at lines 1315--1316 [] [39] Overfull \hbox (94.81851pt too wide) in paragraph at lines 1354--1355 [] [40 <./pwd.png>] [41 <./portainer_demo.png>] [42] Chapter 8. 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Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 2687. [77] [78] Chapter 12. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 2730. [79] [80] Chapter 13. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxstylestrong' on input line 2750. (./CyVerseDocumentation.ind) [81] (./CyVerseDocumentation.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on CyVerseDocumentation.pdf (85 pages, 3666457 bytes). Transcript written on CyVerseDocumentation.log. 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